Issues with the pivot point and scaling
It looks like you have your transform orientation set to &quot;view&quot;. Set it to &quot;global&quot;, select all the vertices you want to level out, and then press S+Z+0. This will level out your selection on the Z axis.
You can apply the transformation while on Object Mode with Ctrl+A, which then will let you decide what kind of transform you want to &quot;freeze&quot;. Remember that you need to be in object mode for this.